I am very glad to use mothur to analyse my 16s rRNA data but after reading through the MiSeq SOP on the following link:
I have one question about the quality trimming.
I couldn’t find any step that is dedicated to trim the fastq files before merging the R1 and R2 reads based on the base quality of fastq files.
Does it mean that there is no need to trim any poor quality bases of fastq files during the whole process? Why?
Many thanks for your help,